eDNA emerging methods
Thanks for introducing microfluidics chips this week. I had never heard of them before. It’s fascinating that someone capitalized on the very small-scale behavior of fluids to extract DNA from a sample. Additionally, the magnet step that attracts only target DNA is amazing. And the ability to combine an extraction and a PCR on one of these chips almost seems too good to be true! How do microfluidics chip extraction yield and PCR results compare to traditional methods?
I am very intrigued by blocking primers, another spectacular expansion of traditional molecular methods. Despite their difficulties, blockers have a lot of potential in preventing one organism from overwhelming a metabarcoding sample! I have been watching Alex Ascher and Pete Countway’s progress on developing lobster blocking primers and it seems to have involved a lot of trial-and-error. Much of the frustration arises from the priming region being highly similar between taxa they want to amplify and the taxon they want to block.
I also appreciated the discussion on PCR alternatives (and fanastic lamp GIFs), as PCR can be prohibitively expensive to some groups. It seems like a well-designed LAMP assay could be a real boon for volunteer researchers and community science organizations, as well as rapid results in the field. While LAMP is a simpler reaction and much faster, the (relative) ease of designing PCR reactions makes PCR appear more versatile to me; however, I have only ever designed and run PCR assays and never used LAMP. I’d be interested to learn more about LAMP primer design, as the quantity of primers to design and its difficultly to be the main drawback of the method over PCR. I am certainly interested in exploring some of these new techniques in the context of eDNA!